New Health challenged the council's decision on the grounds that it had no legal power to do so; if there was power, its exercise by the council was a breach of the right to refuse medical treatment; and council's decision failed to take into account relevant considerations.
But Justice Hansen's ruling rejected all grounds of challenge and cleared the way for council to introduce fluoride to Patea and Waverley water supplies in the 2014-15 financial year.
South Taranaki Mayor Ross Dunlop said he was disappointed and "somewhat surprised" an appeal had been filed given the "thorough ruling".
"New Health NZ's challenge has already consumed a lot of ratepayer dollars and unfortunately it appears that will now continue. The council will of course be seeking to recover whatever costs that it can," Mr Dunlop told the Chronicle.
Meantime, council has delayed fluoridating Patea and Waverley water supplies until the result of the appeal is known.
New Health NZ chairman David Sloan said the High Court was wrong to ignore fundamental human rights and its ruling had worrying implications for all New Zealanders.
"While fluoridation is the only form of mass medication at present, the High Court has effectively paved the way for further such practices," he said.
New Health NZ would argue that the ruling effectively enables councils to use the water supply to deliver chemicals for therapeutic purposes.
"Chemicals for the purpose of birth control, mood disorder and vaccination can be legally added to the water supply at the whim of local authorities," he said.